Removed a warning about the strncpy length.

• Replaced the deprecated boost::split_regex by boost::regex_token_iterator.
• Made sure that configuration script fails if boost is missing

Added the long versions of the residue numbers and chain ids to the hssp file format.

Adds a bugfix, that allows mkdssp and mkhssp to work with large mmCIF files.

Fixes a bug occurring with PDB_REDO files. They have a slightly different SSBOND record.

Makes sure gzip is used even if bzip2 is missing.

Replaced an useless expression to a useful one. in src/hssp-nt.cpp:478.

Changed the hssp3 to hssp1 converter, (hsspconv) so that it adds an extra line SCHAIN, listing the chains that are the same.

• Removed several unused variables and preprocessor directives.
• Made libzeep optional in the configuration. If libzeep is missing, then --fetch-dbrefs is disabled.
• Made the progress module always use std::atomic.

The boost tr1 library was no longer in boost, so we replaced the tr1 tuples with c++ std tuples.